monochrome 2024.3.1__tar.gz → 2024.3.21__tar.gz

{monochrome-2024.3.1 → monochrome-2024.3.21}/.github/workflows/build.yml

@@ -201,43 +201,44 @@ jobs:
           name: python-wheels-sdist
           path: dist/*.tar.gz
 
-  # upload_pypi:
-  #   name: Upload to PyPI
-  #   needs: [test_python_wheels, build_python_sdist]
-  #   runs-on: ubuntu-latest
-  #   environment: pypi
-  #   permissions:
-  #     id-token: write
-  #   if: github.event_name == 'release' && github.event.action == 'published'
-  #   # or, alternatively, upload to PyPI on every tag starting with 'v' (remove on: release above to use this)
-  #   # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
-  #   steps:
-  #     - name: Download artifacts
-  #       uses: actions/download-artifact@v4
-  #       with:
-  #         pattern: python-wheels-*
-  #         path: dist
-  #         merge-multiple: true
-
-  #     - name: Upload to PyPI
-  #       uses: pypa/gh-action-pypi-publish@release/v1
-  #       with:
-  #         repository-url: https://test.pypi.org/legacy/
+  upload_pypi:
+    name: Upload to PyPI
+    needs: [test_python_wheels, build_python_sdist]
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      id-token: write
+    if: github.event_name == 'release' && github.event.action == 'published'
+    # or, alternatively, upload to PyPI on every tag starting with 'v' (remove on: release above to use this)
+    # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          pattern: python-wheels-*
+          path: dist
+          merge-multiple: true
+
+      - name: Upload to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
   
-  # upload_github_release:
-  #   name: Upload to GitHub Releases
-  #   needs: [test_python_wheels, standalone_linux, standalone_windows, standalone_macos]
-  #   runs-on: ubuntu-latest
-  #   if: github.event_name == 'release' && github.event.action == 'published'
-  #   steps:
-  #     - name: Download artifacts
-  #       uses: actions/download-artifact@v4
-  #       with:
-  #         pattern: standalone-*
-  #         path: dist
-  #         merge-multiple: true
-
-  #     - name: Upload release assets
-  #       uses: softprops/action-gh-release@v1
-  #       with:
-  #         files: dist/*
+  upload_github_release:
+    name: Upload to GitHub Releases
+    needs: [test_python_wheels, standalone_linux, standalone_windows, standalone_macos]
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      contents: write
+    if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          pattern: standalone-*
+          path: dist
+          merge-multiple: true
+
+      - name: Upload release assets
+        uses: softprops/action-gh-release@v1
+        with:
+          files: dist/*

monochrome-2024.3.21/PKG-INFO

@@ -0,0 +1,163 @@
+Metadata-Version: 2.1
+Name: monochrome
+Version: 2024.3.21
+Summary: Viewer for monochromatic video data
+Author-Email: Jan Lebert <mail@janlebert.com>
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: POSIX
+Classifier: Programming Language :: C++
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Desktop Environment
+Classifier: Topic :: Multimedia :: Video :: Display
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Project-URL: Documentation, https://monochrome.readthedocs.io
+Project-URL: Repository, https://github.com/sitic/monochrome
+Requires-Python: >=3.6
+Requires-Dist: numpy
+Requires-Dist: flatbuffers>=23.5.26
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinxcontrib-napoleon; extra == "docs"
+Requires-Dist: sphinxcontrib-bibtex; extra == "docs"
+Requires-Dist: sphinxcontrib-video; extra == "docs"
+Requires-Dist: sphinx-autobuild; extra == "docs"
+Requires-Dist: sphinx-copybutton; extra == "docs"
+Requires-Dist: sphinx-codeautolink; extra == "docs"
+Requires-Dist: furo; extra == "docs"
+Requires-Dist: myst_nb>=1.0.0; extra == "docs"
+Requires-Dist: jupytext; extra == "docs"
+Requires-Dist: jupyter-cache; extra == "docs"
+Requires-Dist: sphinx-remove-toctrees; extra == "docs"
+Requires-Dist: sphinx-design; extra == "docs"
+Requires-Dist: enum-tools[sphinx]; extra == "docs"
+Requires-Dist: opticalmapping[all]; extra == "docs"
+Provides-Extra: test
+Provides-Extra: docs
+Description-Content-Type: text/markdown
+
+# Monochrome: Viewer for Monochromatic Video Data
+[![docs](https://readthedocs.org/projects/monochrome/badge/?version=latest&style=)](https://monochrome.readthedocs.org)
+[![tests](https://github.com/sitic/monochrome/actions/workflows/build.yml/badge.svg)](https://github.com/sitic/monochrome/actions/workflows/build.yml)
+[![PyPI](https://img.shields.io/pypi/v/monochrome.svg)](https://pypi.org/project/monochrome/)
+[![Supported Python versions](https://img.shields.io/pypi/pyversions/monochrome.svg)](https://python.org)
+
+Monochrome is a lightweight and fast video viewer for scientific monochromatic videos with high-dynamic range (float, uint16, etc.).
+
+It is designed for viewing high-speed monochromatic fluorescence video data from scientific cameras and meet our specific needs for cardiac optical mapping data (together with [optimap](https://github.com/cardiacvision/optimap)):
+* Support for high-dynamic range (uint16, 32-bit float) data with sliders to adjust intensity range
+* Playback of multiple videos in sync
+* High-speed playback with precise frame-rate control
+* Viewing of optical traces (average intensity in a region of interest over time)
+* Rendering of layers on top of videos with transparency
+* Rendering of point positions over time (e.g. for tracking or optical flow visualization)
+* Exporting videos as a sequence of PNG images or MP4 videos with control over frame rate and frame skipping
+* Cross-platform (Linux, Windows, MacOS)
+
+It is designed to be fast and lightweight, i.e. it uses memory-mapping to load video files to avoid copying the data into RAM.
+
+## Installation
+
+There are two ways to install Monochrome: as a standalone application and/or with its Python interface through pip.
+
+In the standalone application, supported video files can be loaded by drag & drop them into the window or by associating the file extension with Monochrome to open them with a double-click. The Python interface allows to load and play videos from Python scripts and Jupyter notebooks.
+
+### Standalone Application
+
+Download the relevant executable (Windows, macOS, or Linux) from the latest [release page](https://github.com/sitic/monochrome/releases/latest). See the [installation instructions](https://monochrome.readthedocs.io/latest/installation_standalone/) for details.
+
+### Python Library
+
+The Python library includes all necessary files and does not require the installation of the standalone Monochrome application. Open a terminal window and run the following command:
+
+```bash
+python -m pip install monochrome
+```
+
+See the [Python installation guide](https://monochrome.readthedocs.io/latest/installation_python/) for further details. To start the viewer in standalone mode, run:
+```bash
+python -m monochrome
+```
+
+See the [tutorial](https://monochrome.readthedocs.io/latest/tutorial/) for an introduction to the Python library, here is a brief overview:
+
+```python
+import monochrome as mc
+import numpy as np
+
+# Create some video with shape (time, height, width) as a numpy array
+video = np.random.rand(500, 256, 256)
+
+# Display the video, see the tutorial for more details and options.
+# Monochrome should automatically start and show the video in a loop.
+mc.show_video(video, name="First Video", cmap='viridis', vmin=0, vmax=1)
+
+# Play second video in sync with the first (note that the videos should have the same length)
+video2 = (np.random.rand(500, 256, 256) * 65535).astype(dtype=np.uint16)
+mc.show_video(video2, name="Second Video", comment="This is a uint16 video", bitrange="uint16")
+# `bitrange` argument is optional, Monochrome will auto-detect the data type
+
+# Layers can be added on top of video
+overlay = np.random.rand(500, 256, 256)
+overlay[:, 64:192, :] = np.nan # NaN values will be transparent pixels, see tutorial
+mc.show_layer(overlay, parent="Second Video", cmap='PRGn', opacity='centered')
+
+# List of functions:
+# mc.show() is a shortcut for mc.show_video()/show_layer()/show_image()/show_file(),
+#           it will try to auto-detect the input type and call the appropriate function.
+# mc.show_video() to show videos
+# mc.show_image() to show single images
+# mc.show_layer() to show layers on top of videos/images
+# mc.show_points() to visualize point positions over time over videos
+# mc.show_flow() to visualize optical flow fields over time
+# mc.show_file() to load videos from file in Monochrome
+# mc.launch() to start Monochrome from Python
+```
+
+## Native Video File Formats
+Monochrome supports loading the following video file formats:
+
+* `.npy`, NumPy array with shape (time, width, height). The data type can be float (np.float32, np.float64), integer (uint8, uint16, etc.), or boolean.
+* `.dat`, raw binary file with shape (time, width, height) and data type float32
+* `.dat`, MultiRecorder file format (used in the cardiac optical mapping community)
+
+Drag & drop the file into the window or associate the file extension with Monochrome to open it with a double-click.
+
+## Usage & Key Bindings
+
+Adjust settings for each video in the main control window. To view optical traces (average intensity in a region of interest over time), click in a video. Click and drag to move the region of interest. Right-click to remove the region of interest.
+
+Keyboard shortcuts:
+
+| Keybinding &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; | Action &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; |
+| --- | --- |
+| `Ctrl + q` | Quit Monochrome |
+| `Esc` or `q` | Close focused recording |
+| `Space` | Play/Pause |
+| `Up` | Increase playback speed (frame skip) |
+| `Down` | Decrease playback speed (frame skip) |
+| `0` or `r` | Reset playback to beginning |
+| `Left` | Skip to next frame |
+| `Right` | Skip to previous frame |
+| `Shift + Left` | 10x previous frame |
+| `Shift + Right` | 10x next frame |
+| `Ctrl + Left` | Previous frame in focused recording only |
+| `Ctrl + Right` | Next frame in focused recording only |
+| `Ctrl + Left + Shift` | 10x previous frame in focused recording only |
+| `Ctrl + Right + Shift` | 10x next frame in focused recording only |
+| `p` | Save screenshot of focused recording |
+| `s` | Sync playback of all recordings |
+
+## Additional Resources
+
+* [Documentation](https://monochrome.readthedocs.io)
+* [Python Tutorial](https://monochrome.readthedocs.io/latest/tutorial/)
+* [PyPI package](https://pypi.org/project/monochrome/)
+* [GitHub repository](https://github.com/sitic/monochrome)
+
+## License
+
+Monochrome is licensed under the MIT License.

monochrome-2024.3.21/README.md

@@ -0,0 +1,122 @@
+# Monochrome: Viewer for Monochromatic Video Data
+[![docs](https://readthedocs.org/projects/monochrome/badge/?version=latest&style=)](https://monochrome.readthedocs.org)
+[![tests](https://github.com/sitic/monochrome/actions/workflows/build.yml/badge.svg)](https://github.com/sitic/monochrome/actions/workflows/build.yml)
+[![PyPI](https://img.shields.io/pypi/v/monochrome.svg)](https://pypi.org/project/monochrome/)
+[![Supported Python versions](https://img.shields.io/pypi/pyversions/monochrome.svg)](https://python.org)
+
+Monochrome is a lightweight and fast video viewer for scientific monochromatic videos with high-dynamic range (float, uint16, etc.).
+
+It is designed for viewing high-speed monochromatic fluorescence video data from scientific cameras and meet our specific needs for cardiac optical mapping data (together with [optimap](https://github.com/cardiacvision/optimap)):
+* Support for high-dynamic range (uint16, 32-bit float) data with sliders to adjust intensity range
+* Playback of multiple videos in sync
+* High-speed playback with precise frame-rate control
+* Viewing of optical traces (average intensity in a region of interest over time)
+* Rendering of layers on top of videos with transparency
+* Rendering of point positions over time (e.g. for tracking or optical flow visualization)
+* Exporting videos as a sequence of PNG images or MP4 videos with control over frame rate and frame skipping
+* Cross-platform (Linux, Windows, MacOS)
+
+It is designed to be fast and lightweight, i.e. it uses memory-mapping to load video files to avoid copying the data into RAM.
+
+## Installation
+
+There are two ways to install Monochrome: as a standalone application and/or with its Python interface through pip.
+
+In the standalone application, supported video files can be loaded by drag & drop them into the window or by associating the file extension with Monochrome to open them with a double-click. The Python interface allows to load and play videos from Python scripts and Jupyter notebooks.
+
+### Standalone Application
+
+Download the relevant executable (Windows, macOS, or Linux) from the latest [release page](https://github.com/sitic/monochrome/releases/latest). See the [installation instructions](https://monochrome.readthedocs.io/latest/installation_standalone/) for details.
+
+### Python Library
+
+The Python library includes all necessary files and does not require the installation of the standalone Monochrome application. Open a terminal window and run the following command:
+
+```bash
+python -m pip install monochrome
+```
+
+See the [Python installation guide](https://monochrome.readthedocs.io/latest/installation_python/) for further details. To start the viewer in standalone mode, run:
+```bash
+python -m monochrome
+```
+
+See the [tutorial](https://monochrome.readthedocs.io/latest/tutorial/) for an introduction to the Python library, here is a brief overview:
+
+```python
+import monochrome as mc
+import numpy as np
+
+# Create some video with shape (time, height, width) as a numpy array
+video = np.random.rand(500, 256, 256)
+
+# Display the video, see the tutorial for more details and options.
+# Monochrome should automatically start and show the video in a loop.
+mc.show_video(video, name="First Video", cmap='viridis', vmin=0, vmax=1)
+
+# Play second video in sync with the first (note that the videos should have the same length)
+video2 = (np.random.rand(500, 256, 256) * 65535).astype(dtype=np.uint16)
+mc.show_video(video2, name="Second Video", comment="This is a uint16 video", bitrange="uint16")
+# `bitrange` argument is optional, Monochrome will auto-detect the data type
+
+# Layers can be added on top of video
+overlay = np.random.rand(500, 256, 256)
+overlay[:, 64:192, :] = np.nan # NaN values will be transparent pixels, see tutorial
+mc.show_layer(overlay, parent="Second Video", cmap='PRGn', opacity='centered')
+
+# List of functions:
+# mc.show() is a shortcut for mc.show_video()/show_layer()/show_image()/show_file(),
+#           it will try to auto-detect the input type and call the appropriate function.
+# mc.show_video() to show videos
+# mc.show_image() to show single images
+# mc.show_layer() to show layers on top of videos/images
+# mc.show_points() to visualize point positions over time over videos
+# mc.show_flow() to visualize optical flow fields over time
+# mc.show_file() to load videos from file in Monochrome
+# mc.launch() to start Monochrome from Python
+```
+
+## Native Video File Formats
+Monochrome supports loading the following video file formats:
+
+* `.npy`, NumPy array with shape (time, width, height). The data type can be float (np.float32, np.float64), integer (uint8, uint16, etc.), or boolean.
+* `.dat`, raw binary file with shape (time, width, height) and data type float32
+* `.dat`, MultiRecorder file format (used in the cardiac optical mapping community)
+
+Drag & drop the file into the window or associate the file extension with Monochrome to open it with a double-click.
+
+## Usage & Key Bindings
+
+Adjust settings for each video in the main control window. To view optical traces (average intensity in a region of interest over time), click in a video. Click and drag to move the region of interest. Right-click to remove the region of interest.
+
+Keyboard shortcuts:
+
+| Keybinding         | Action                |
+| --- | --- |
+| `Ctrl + q` | Quit Monochrome |
+| `Esc` or `q` | Close focused recording |
+| `Space` | Play/Pause |
+| `Up` | Increase playback speed (frame skip) |
+| `Down` | Decrease playback speed (frame skip) |
+| `0` or `r` | Reset playback to beginning |
+| `Left` | Skip to next frame |
+| `Right` | Skip to previous frame |
+| `Shift + Left` | 10x previous frame |
+| `Shift + Right` | 10x next frame |
+| `Ctrl + Left` | Previous frame in focused recording only |
+| `Ctrl + Right` | Next frame in focused recording only |
+| `Ctrl + Left + Shift` | 10x previous frame in focused recording only |
+| `Ctrl + Right + Shift` | 10x next frame in focused recording only |
+| `p` | Save screenshot of focused recording |
+| `s` | Sync playback of all recordings |
+
+## Additional Resources
+
+* [Documentation](https://monochrome.readthedocs.io)
+* [Python Tutorial](https://monochrome.readthedocs.io/latest/tutorial/)
+* [PyPI package](https://pypi.org/project/monochrome/)
+* [GitHub repository](https://github.com/sitic/monochrome)
+
+## License
+
+Monochrome is licensed under the MIT License.

monochrome-2024.3.21/docs/development.md

@@ -0,0 +1,58 @@
+# Contributing to Monochrome
+
+Contributions are welcome! This document describes how to set up a development environment and how to contribute to the project.
+
+## Installing from Source
+
+Clone the repository and install the dependencies.
+
+```bash
+git clone https://github.com/sitic/monochrome.git
+cd monochrome
+```
+
+### Dependencies
+
+#### Linux
+
+Install the following packages:
+```bash
+sudo apt install build-essential cmake mesa-utils xorg-dev
+```
+
+#### MacOS
+
+Download [CMake](https://cmake.org/download/) and Xcode.
+
+#### Windows
+
+Download [CMake](https://cmake.org/) and a C++ compiler like Microsoft Visual C++.
+
+### Compilation
+
+#### Standalone Application
+
+This project uses CMake to generate cross-platform build configurations.
+
+```bash
+# Create a build subfolder
+mkdir build
+cd build
+
+# Generate a project for the default platform
+cmake ..
+
+# Then use your IDE or use CMake to compile
+cmake --build .
+
+# Linux only: installation
+sudo cmake --build . --target install
+```
+
+#### Python Version
+
+Alternatively, you can build the Python package which includes builing Monochrome with the following command:
+
+```bash
+python -m pip install .
+```

{monochrome-2024.3.1 → monochrome-2024.3.21}/docs/index.md

@@ -1,15 +1,13 @@
-```{toctree}
-:maxdepth: 3
-:hidden:
-
-Introduction & Installation <self>
-```
-
 ```{toctree}
 :maxdepth: 2
 :hidden:
 
-API Reference <api/monochrome>
+Introduction <self>
+installation_standalone
+installation_python
+tutorial
+development
+Python API Reference <api/monochrome>
 ```
 
 % Generate API reference

monochrome-2024.3.21/docs/installation_python.md

@@ -0,0 +1,24 @@
+# Installing the Python Interface
+
+```{note}
+The installation of the standalone Monochrome application is **not** required, as the Python library includes all necessary files.
+```
+
+Run the following command to install Monochrome with the included Python library:
+
+```bash
+python -m pip install monochrome
+```
+
+On Windows you might need to run
+```bash
+py -m pip install monochrome
+```
+
+Run
+```bash
+python -m monochrome
+```
+to start the viewer in standalone mode.
+
+See the [tutorial](tutorial) for a quick introduction to the Python library.

monochrome-2024.3.21/docs/installation_standalone.md

@@ -0,0 +1,22 @@
+# Installing the Standalone Version
+
+## Windows
+
+Download `Monochrome.exe` from the [latest release](https://github.com/sitic/monochrome/releases/latest) and run it. You may need to install [Microsoft Visual C++ Redistributable 2019](https://aka.ms/vs/16/release/vc_redist.x86.exe) if you get an error about missing `VCRUNTIME140_1.dll`.
+
+```{figure} /_static/Windows_Install.png
+:class: bg-primary
+:width: 75%
+:align: center
+:alt: Windows Defender SmartScreen warning
+
+Because Monochrome is not digitally signed, Windows Defender might show a warning when you try to launch it. This is normal. To proceed, click on "More info" and then "Run anyway".
+```
+
+## macOS
+
+Download the `.dmg` file from the [latest release](https://github.com/sitic/monochrome/releases/latest) and run it to copy `Monochrome.app` to your Applications folder. When launching Monochrome for the first time, you may need to right-click on the app in Finder and select "Open" to bypass the security warning. For more information, see the "[open a Mac app from an unidentified developer](https://support.apple.com/guide/mac-help/open-a-mac-app-from-an-unidentified-developer-mh40616/mac)" guide from Apple.
+
+## Linux
+
+Download the `.AppImage` file from the [latest release](https://github.com/sitic/monochrome/releases/latest) and run it. You may need to mark the file as executable, see the [AppImage documentation](https://docs.appimage.org/introduction/quickstart.html) for more information.

monochrome-2024.3.21/docs/tutorial.ipynb

@@ -0,0 +1,115 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Python Tutorial\n",
+    "\n",
+    "```{note}\n",
+    "\n",
+    "This tutorial is currently in preparation. Please check back later.\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import monochrome as mc\n",
+    "import optimap as om"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "filename = om.utils.retrieve_example_data(\"Example_02_VF_Rabbit_Di-4-ANEPPS_Basler_acA720-520um.npy\")\n",
+    "video = om.load_video(filename)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mc.show(video, name=\"Example Recording\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Several videos can be shown at the same time, they will be played in sync if they have the same length:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Converting video to np.float32 with values between 0 and 1\n",
+    "video2 = om.video.normalize(video)\n",
+    "print(f\"Video shape: {video2.shape}, dtype: {video2.dtype}\")\n",
+    "\n",
+    "# vmin and vmax are optional and used to set the minimum and maximum values of the colormap\n",
+    "mc.show(video2, name=\"Another Recording\", cmap=\"viridis\", vmin=0.1, vmax=0.9)\n",
+    "mc.show(video2[0], name=\"First Frame\", cmap=\"gray\", vmin=0.1, vmax=0.9)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The functions {func}`show` or {func}`show_file` can be used to load a video from a file in Monochrome:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print(filename)\n",
+    "mc.show(filename)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "om.motion_compensate"
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